[1]} used path sampling to compare
models of amino-acid substitution.
They found that the harmonic mean estimator favored the most parameter rich
model for all five datasets they explored, whereas the path-sampling estimates
favored simpler models for three of the datasets.
This again demonstrates that accurately estimated marginal likelihoods can
indeed “penalize” for over-parameterization of phylogenetic models.
More importantly, this work also revealed that modeling heterogeneity in amino
acid composition across sites of an alignment better explains the variation in
biological data.
